To effectively reduce CO2 emissions, it’s vital to identify and quantify their sources. While the focus has been on CO2 from fossil fuel combustion, especially coal, the CO2 produced from coal’s other elements, such as sulfur, through chemical reaction, remains an ‘invisible’ carbon source. We analyzed the invisible carbon flux due to coal burning in the Xijiang River Basin, a highly industrialized region in China, using river sulfate fluxes. Dissolved sulfate concentration in the Xijiang River rose by over 300% from 1985 to 2011, largely due to coal combustion. In 2011, this resulted in 3.14 Mt of invisible carbon dioxide. We evaluated the impact of two flue gas desulfurization (FGD) methods on carbon emissions using a predictive model. By enhancing SO2 removal efficiency through these methods, China could cut invisible carbon emissions by 27.8 Mt CO2 annually, paving the way for a sustainable future.